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D7.5: HPC Programming Techniques

Cevdet Aykanat, Antun Balaz, Iris Christadler, Ivan Girotto, Jose Gracia, Vladimir Slavnic, Andy Sunderland, Ata Türk
2012 Zenodo  
Task 7.5 worked on five different areas to increase performance and scalability of user codes: Scalable algorithms Scalable libraries Multi-core/many core systems Accelerators Novel HPC languages Overall  ...  It consists of chapters for each of the five topics, containing high-level summaries of all projects. In most of th [...]  ...  CP2K is a state-of-the-art tool used in atomistic and molecular simulations of solid state, liquid, molecular and biological systems and it employs a new linear-scaling self-consistent field (SCF) method  ... 
doi:10.5281/zenodo.6552939 fatcat:z2gdhmnojrh6bj2lordyl7lmnq

An introduction to the xSDK, a community of diverse numerical HPC software packages [article]

Ulrike Yang, XSDK Developers
2019 Figshare  
Extreme-scale computational science increasingly demands multiscale and multiphysics formulations, which in turn require many high-quality, robust, portable high-performance math libraries.  ...  HPC community—that provide the building blocks, tools, models, processes, and related artifacts for rapid and efficient development of high-quality applications.  ...  Terrestrial ecosystem use cases tie IDEAS to modeling and simulation goals in two Science Focus Area (SFA) programs and both Next Generation Ecosystem Experiment (NGEE) programs in DOE Biologic and Environmental  ... 
doi:10.6084/m9.figshare.7779452 fatcat:5yf35t4nyjailptpdtgdk2lboy

D7.2.2 Exploitation of HPC Tools and Techniques

Michael Lysaght, Bjorn Lindi, Vit Vondrak, John Donners, Marc Tajchman
2014 Zenodo  
In this sense, the report here follows on naturally from the T7.2 deliverable D7.2.1, 'A Report on the Survey of HPC Tools and Techniques', which represented the first phase of activity in T7.2.  ...  These are: (1) Programming Models, (2) Scalable Libraries and Algorithms, (3) Debuggers and Profilers and finally, (4) I/O Management Techniques.  ...  It provides a flexible, portable and scalable set of technologies for performance evaluation on extreme-scale HPC systems.  ... 
doi:10.5281/zenodo.6575525 fatcat:5y3cjsculrdejllndosbjpcgiq

StreamFlow: cross-breeding cloud with HPC [article]

Iacopo Colonnelli, Barbara Cantalupo, Ivan Merelli, Marco Aldinucci
2020 arXiv   pre-print
Many of them target a specific environment; few of them make it possible to execute an entire workflow in different environments, e.g. Kubernetes and batch clusters.  ...  Workflows are among the most commonly used tools in a variety of execution environments.  ...  Acknowledgment This article describes work undertaken in the context of the Deep-Health project, "Deep-Learning and HPC to Boost Biomedical Applications for Health" (https://deephealth-project.eu/) which  ... 
arXiv:2002.01558v2 fatcat:jywyqbvx6vggxfwjzv5mkvgaxe

DARPA's HPCS Program: History, Models, Tools, Languages [chapter]

Jack Dongarra, Robert Graybill, William Harrod, Robert Lucas, Ewing Lusk, Piotr Luszczek, Janice Mcmahon, Allan Snavely, Jeffrey Vetter, Katherine Yelick, Sadaf Alam, Roy Campbell (+5 others)
2008 Advances in Computers  
Developing the Evaluation Tools 7 A prerequisite for the scientific and quantified study of productivity in HPC systems is the development of tools and protocols to study productivity.  ...  As a way to understand the particular needs of HPC programmers, prototype tools were developed in Phases 1 and 2 of the HPCS program to study productivity in the HPC community.  ... 
doi:10.1016/s0065-2458(08)00001-6 fatcat:ilchf26s2fgkzlnqplxt243u7m

HPC Infrastructures Workshop 2021

Gert Svensson
2021 Zenodo  
the latest trends in HPC infrastructure and supporting technologies for supercomputing centres.  ...  The 11th EWHPC event was held on the 18th and 19th of May 2021 and was followed, as usual, by a PRACE session on HPC infrastructures.  ...  Acknowledgements This work was financially supported by the PRACE project funded in part by the EU's Horizon 2020 Research and Innovation programme (2014-2020) under grant agreement 823767.  ... 
doi:10.5281/zenodo.5794766 fatcat:p3phw2u6vzfjxoutydphkf4x3m

Eurolab-4-HPC Long-Term Vision on High-Performance Computing [article]

Theo Ungerer, Paul Carpenter
2018 arXiv   pre-print
, software, and applications in High-Performance Computing (HPC).  ...  This document presents the "EuroLab-4-HPC Long-Term Vision on High-Performance Computing" of August 2017, a road mapping effort within the EC CSA1 Eurolab-4-HPC that targets potential changes in hardware  ...  Such abstractions greatly improve programmer productivity and portability across systems.  ... 
arXiv:1807.04521v1 fatcat:5neetrgubjhnvcajcktpkohrzq

D5.3: HPC Infrastructures Workshop #8

Huub Stoffers
2017 Zenodo  
The 8th European Workshop on HPC Centre Infrastructures was organised by CSCS and held in Mendrisio, a town near Lugano, Switzerland, between April 5, 2017 – April 7, 2017.  ...  The workshop covered a broad range of topics relevant for HPC Centre Infrastructure management: standards and regulations, energy effciency strategies, total cost of ownership reduction strategies, energy  ...  The pilot systems will be tested on benchmarks from the UEABS selected for their scalability, active development and portability to hybrid machines.  ... 
doi:10.5281/zenodo.6805971 fatcat:rkbmbos4qzhupm5bzqvo7q5dsi

Translational research design templates, Grid computing, and HPC

Joel Saltz, Scott Oster, Shannon Hastings, Stephen Langella, Renato Ferreira, Justin Permar, Ashish Sharma, David Ervin, Tony Pan, Umit Catalyurek, Tahsin Kurc
2008 Proceedings, International Parallel and Distributed Processing Symposium (IPDPS)  
Using caGrid, which is a Grid middleware system based on the model driven architecture (MDA) and the service oriented architecture (SOA) paradigms, as a starting point, we discuss architecture directions  ...  Design templates that involve discovery, analysis, and integration of information resources commonly occur in many scientific research projects.  ...  The Multiscale Template models studies that attempt to measure, quantify, and in some cases simulate, biomedical phenomena in a way that takes into account multiple spatial and/or temporal scales.  ... 
doi:10.1109/ipdps.2008.4536089 pmid:21311740 pmcid:PMC3035416 dblp:conf/ipps/SaltzOHLFPSEPCK08 fatcat:c4id7bjtd5ebpkrtmgfteiykuy

D5.3: Updated Best Practices for HPC Procurement and Infrastructure

Andreas Johansson
2014 Zenodo  
WP5 provides input for defining and updating procurement plans and strategies through the sharing of the state of the art and best practices in procuring and operating production HPC systems.  ...  Specific areas of interest are analysed in depth in terms of the market they belong to and the general HPC landscape, with a particular emphasis on the European point of view.  ...  hosting HPC facilities and supercomputing infrastructures (the Consorci Centre de Serveis Cientifics i Academics de Catalunya, CESCA in Spain and the group HKNR in LUH).  ... 
doi:10.5281/zenodo.6572433 fatcat:cwiqrgf33jajjjvhubky4f6rau

Fast and Accurate CBR Defense for Homeland Security: Bringing HPC to the First Responder and Warfighter

G. Patnaik, J. Boris
2007 2007 DoD High Performance Computing Modernization Program Users Group Conference  
, or in the airborne Chemical, Biological, and Radiological (CBR) context of crisis management after terrorist attacks or threats, called CT-Analyst® and based on new principles, accidents in urban environments  ...  models is made in the licensing of new industrial plants, in safety analysis studies for accidental releases of An urban-oriented emergency assessment system for hazardous materials in the chemical industry  ...  data and a unsteady, time-dependent simulation models. typical mesh contains approximately 200 million nodes and 55 million tetrahedral elements.  ... 
doi:10.1109/hpcmp-ugc.2007.33 fatcat:uyth25tnnbdjhmusjyv35f7cea

Towards a HPC-oriented parallel implementation of a learning algorithm for bioinformatics applications

Gianni D'Angelo, Salvatore Rampone
2014 BMC Bioinformatics  
High Performance Computing (HPC) appears as a magic bullet in this challenge. However, several hard to solve parallelization and load balancing problems arise in this context.  ...  Here we discuss the HPC-oriented implementation of a general purpose learning algorithm, originally conceived for DNA analysis and recently extended to treat uncertainty on data (U BRAIN).  ...  The authors wish to thank the CRESCO/ENEAGRID High Performance Computing staff and in particular Ing. Silvio Migliori, Ing. Antonio Perozziello, and Ing. Guido Guarnieri.  ... 
doi:10.1186/1471-2105-15-s5-s2 pmid:25077818 pmcid:PMC4095002 fatcat:bff2nmoourczzplvnykxlqqpra

StreamBrain: An HPC Framework for Brain-like Neural Networks on CPUs, GPUs and FPGAs [article]

Artur Podobas, Martin Svedin, Steven W. D. Chien, Ivy B. Peng, Naresh Balaji Ravichandran, Pawel Herman, Anders Lansner, Stefano Markidis
2021 arXiv   pre-print
StreamBrain is a domain-specific language (DSL), similar in concept to existing machine learning (ML) frameworks, and supports backends for CPUs, GPUs, and even FPGAs.  ...  The modern deep learning method based on backpropagation has surged in popularity and has been used in multiple domains and application areas.  ...  The computations were enabled by resources provided by the Swedish National Infrastructure for Computing (SNIC) at PDC and HPC2N and partially funded by the Swedish Research Council through grant agreement  ... 
arXiv:2106.05373v1 fatcat:zjy73e22wzborpptp3um6ynmem

Addressing the Complexity of HPC in the Cloud: Emergence, Self-Organisation, Self-Management, and the Separation of Concerns [chapter]

Theo Lynn
2018 Heterogeneity, High Performance Computing, Self-Organization and the Cloud  
This chapter introduces cloud computing, HPC, and the challenges of supporting HPC in the cloud.  ...  Three illustrative application scenarios for HPC in the cloud-(i) oil and gas exploration, (ii) ray tracing, and (iii) genomics-are discussed.  ...  Relatively small efficiency and accuracy gains in simulations in the oil and gas industry can result in disproportionately large benefits in terms of European employment and Gross Domestic Product (GDP  ... 
doi:10.1007/978-3-319-76038-4_1 fatcat:mghwrgbdingxbmzz7fbsvlnrfq

ExaWorks: Workflows for Exascale [article]

Aymen Al-Saadi, Dong H. Ahn, Yadu Babuji, Kyle Chard, James Corbett, Mihael Hategan, Stephen Herbein, Shantenu Jha, Daniel Laney, Andre Merzky, Todd Munson, Michael Salim (+3 others)
2021 arXiv   pre-print
Exascale computers will offer transformative capabilities to combine data-driven and learning-based approaches with traditional simulation applications to accelerate scientific discovery and insight.  ...  We present the ExaWorks project, which can address many of these challenges: ExaWorks is leading a co-design process to create a workflow software development Toolkit (SDK) consisting of a wide range of  ...  We thank Rafael Ferreira da Silva and Henri Casanova of the Workflows-RI project for partnering to organize community summits.  ... 
arXiv:2108.13521v1 fatcat:y4qe4oxscbfhhkgydqz7lft3cq
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